Document Type

Dissertation

Degree

Doctor of Philosophy

Major

Biology

Date of Defense

11-29-2022

Graduate Advisor

Patricia G. Parker, PhD

Co-Advisor

Lon M. Chubiz, PhD

Committee

Robert J. Marquis, PhD

Peter O. Dunn, PhD

Abstract

Wild birds are teeming with microorganisms, ranging from commensal bacteria to eukaryotic parasites. These microbes impact host health in diverse ways; some long-term residents may aid digestion or provide immune system training, while others at times may induce disease. However, the factors driving the varying colonization patterns seen across taxa are still not fully understood, and wild avian populations are particularly understudied when compared to mammalian or domesticated systems. This work examines the relative importance of genetic and environmental factors driving microbiome composition and function in wild birds. We collected fecal and blood samples from Galapagos penguins (Spheniscus mendiculus) in Ecuador, and from Eurasian tree sparrows (Passer montanus) in the United States, screened all samples for blood parasites, and used a combination of targeted amplicon sequencing and whole genome sequencing to characterize the composition and function of the gut microbiome. We additionally used targeted amplicon sequencing to characterize major histocompatibility complex diversity in the Eurasian tree sparrow. Results showed that: (1) environmental and demographic factors drive microbial community structure in terms of alpha diversity, beta diversity, and differential abundance, particularly in the sparrow system with high environmental heterogeneity, (2) both gut pathogens and blood parasites are associated with significant shifts in microbial community structure, although putative bacterial pathogens in the gut are associated with the strongest variation in both community structure and function, and (3) genetic variation at immune system loci is associated with the Eurasian tree sparrow gut microbiome in terms of MHC diversity, but this relationship is generally outweighed by other drivers in this system. Using a metagenomic approach across two distinct systems, this work provides greater insight into the role the gut microbiome plays in avian health by demonstrating significant associations with disease status and immunogenetics.

Download

Share

COinS